Incidental Mutation 'IGL02862:Shmt2'
ID 362184
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Shmt2
Ensembl Gene ENSMUSG00000025403
Gene Name serine hydroxymethyltransferase 2 (mitochondrial)
Synonyms 2700043D08Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL02862
Quality Score
Status
Chromosome 10
Chromosomal Location 127352992-127358313 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 127354743 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Glutamine at position 311 (R311Q)
Ref Sequence ENSEMBL: ENSMUSP00000151616 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026470] [ENSMUST00000035735] [ENSMUST00000219239]
AlphaFold Q9CZN7
Predicted Effect probably benign
Transcript: ENSMUST00000026470
AA Change: R314Q

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000026470
Gene: ENSMUSG00000025403
AA Change: R314Q

DomainStartEndE-ValueType
Pfam:SHMT 49 448 5.4e-211 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000035735
SMART Domains Protein: ENSMUSP00000042185
Gene: ENSMUSG00000040280

DomainStartEndE-ValueType
Pfam:B12D 16 84 2.5e-32 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000217682
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218035
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218258
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218302
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218313
Predicted Effect probably benign
Transcript: ENSMUST00000219239
AA Change: R311Q

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218492
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220356
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit lethlity after E13.5, decreased size, anemia and reduced MEF cellular respiration and proliferation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 26 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actn4 A G 7: 28,611,659 (GRCm39) probably benign Het
Adhfe1 T C 1: 9,624,036 (GRCm39) L170P probably damaging Het
Adprh C T 16: 38,266,396 (GRCm39) V249I probably benign Het
Akr1e1 T C 13: 4,659,092 (GRCm39) T11A possibly damaging Het
Arhgap23 A G 11: 97,347,306 (GRCm39) E668G probably damaging Het
Ccdc163 G A 4: 116,569,910 (GRCm39) probably null Het
Egfr A T 11: 16,833,562 (GRCm39) Y610F probably benign Het
Ercc3 T C 18: 32,376,255 (GRCm39) probably null Het
Fasn G T 11: 120,709,805 (GRCm39) H417Q possibly damaging Het
Gjd2 A G 2: 113,843,624 (GRCm39) probably benign Het
Grip2 C T 6: 91,765,085 (GRCm39) R59H probably damaging Het
H2bc11 C T 13: 22,227,515 (GRCm39) S39L possibly damaging Het
Ighv1-43 A G 12: 114,909,859 (GRCm39) V21A probably damaging Het
Ltbp1 G A 17: 75,697,466 (GRCm39) G1368D probably damaging Het
Mogs G T 6: 83,092,871 (GRCm39) G104C probably damaging Het
Nfix T A 8: 85,440,475 (GRCm39) T472S probably benign Het
Or5m9 T C 2: 85,877,648 (GRCm39) V274A probably benign Het
Ovch2 A T 7: 107,394,138 (GRCm39) V105E probably damaging Het
Pex1 G T 5: 3,655,424 (GRCm39) probably benign Het
Pkd1l2 G A 8: 117,792,484 (GRCm39) T436I probably benign Het
Prl7a1 T C 13: 27,823,872 (GRCm39) T70A probably benign Het
St3gal4 A G 9: 34,963,543 (GRCm39) I255T probably benign Het
Taf8 C T 17: 47,805,339 (GRCm39) A187T probably damaging Het
Tm6sf1 T A 7: 81,520,504 (GRCm39) V62D probably damaging Het
Trpm5 A T 7: 142,636,262 (GRCm39) W537R probably damaging Het
Vmn2r101 T A 17: 19,831,867 (GRCm39) L621H probably damaging Het
Other mutations in Shmt2
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0057:Shmt2 UTSW 10 127,356,917 (GRCm39) missense possibly damaging 0.88
R0057:Shmt2 UTSW 10 127,356,917 (GRCm39) missense possibly damaging 0.88
R0504:Shmt2 UTSW 10 127,355,941 (GRCm39) missense probably damaging 1.00
R1493:Shmt2 UTSW 10 127,354,812 (GRCm39) splice site probably null
R2006:Shmt2 UTSW 10 127,355,029 (GRCm39) missense probably benign 0.22
R2342:Shmt2 UTSW 10 127,354,680 (GRCm39) missense possibly damaging 0.94
R2358:Shmt2 UTSW 10 127,353,897 (GRCm39) missense probably benign 0.00
R4352:Shmt2 UTSW 10 127,354,686 (GRCm39) missense probably damaging 0.97
R4998:Shmt2 UTSW 10 127,354,139 (GRCm39) missense probably damaging 1.00
R5242:Shmt2 UTSW 10 127,354,789 (GRCm39) missense probably benign 0.00
R5568:Shmt2 UTSW 10 127,356,250 (GRCm39) missense probably damaging 1.00
R5654:Shmt2 UTSW 10 127,353,668 (GRCm39) missense probably benign 0.05
R6167:Shmt2 UTSW 10 127,353,731 (GRCm39) missense probably benign
R8465:Shmt2 UTSW 10 127,355,945 (GRCm39) missense probably damaging 1.00
R8503:Shmt2 UTSW 10 127,354,789 (GRCm39) missense probably benign 0.00
R8776:Shmt2 UTSW 10 127,356,785 (GRCm39) critical splice donor site probably null
R8776-TAIL:Shmt2 UTSW 10 127,356,785 (GRCm39) critical splice donor site probably null
R9099:Shmt2 UTSW 10 127,355,962 (GRCm39) missense possibly damaging 0.86
R9124:Shmt2 UTSW 10 127,355,561 (GRCm39) missense possibly damaging 0.88
Z1176:Shmt2 UTSW 10 127,355,347 (GRCm39) missense possibly damaging 0.46
Z1177:Shmt2 UTSW 10 127,356,804 (GRCm39) nonsense probably null
Posted On 2015-12-18